Please use formatting for terminal dumps; it makes them infinitely more readable 
All of these suggest that despite the “uninstallation” of SGE, and the unsetting of SGE_ROOT, FSL is still trying to execute FIRST using SGE. This is outside of the scope of MRtrix3, and I don’t know what internal logic is used when that script is run to decide how to execute the underlying commands. It might be possible that the FSL configuration script is setting something that causes SGE to be used?
Otherwise, even if running with SGE, it should still be possible to get more insight: while the .vtk files are absent, there should be some text files in the script directory that contain the stdout and stderr contents of the individual jobs. These should contain some indication of why the commands are failing.
I would also suggest reading this PR. The behaviour has not yet been changed in MRtrix3 (this will happen with the next update), but the fact that the fsl5.0-* commands are being invoked may be indicative of a setup issue. These files should not appear in PATH, and the FSL configuration script should be used.
Rob